AMBER Archive (2007)

Subject: Re: AMBER: interaction energy calculations

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Tue Oct 09 2007 - 15:51:25 CDT

Gurpreet,

I am not the strongest on this topic but from what I remember anal will
create the number of groups according to those specificed and all others.
So from your output it appears that group 1 is Residue 50, group 2 is
Residue 146, and group 3 is everything else. Of course, I am willing to be
corrected by someone more knowledgeable about anal.

Good luck,

Scott

On 10/9/07, gurpreet singh <gps.iitm_at_gmail.com> wrote:
>
> Hello Amber users
>
> I am using Anal module for calculating the interaction energy between some
> specific residues using the following input file
>
> ..............................................
> 1 0 0 0 0 1
> 0 0.0 0.0 0.0 0.0
> 1 0 0 0 0 0
> 99.0 2.0 1.2 1.0
> 1 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0
> ENERGY
> first residue
> RES 50
> END
> second residue (or group of atoms)
> RES 146
> END
> END
> STOP
> ......................................
>
> In this file I am using two groups i,e RES 50 and RES 146 i.e I want the
> interaction energy between these two groups but in the ouput file it is
> showing total number of groups one more than the this ie 3 for this case
> look at the output below
>
>
>
>
> ..................................................
>
>
> VDW (N-B + 1-4) INTERACTION ENERGY MATRIX
>
>
>
>
> 1 2 3
> 1 5.369 -0.032 -4.946
> 2 -0.032 5.388***********
> 3 -4.946*********** 2064.981
>
> INDIVIDUAL GROUPS INTERACTION
>
>
>
> GROUP INTRA INTER TOTAL
>
> 1 5.37 -4.98 0.39
> 2 5.39**********************
> 3 2064.98**********************
>
>
> TOTAL 2075.74**********************
>
>
> ELECTROSTATIC (N-B + 1-4) INTERACTION ENERGY MATRIX
>
>
>
>
> 1 2 3
> 1 5.177 0.121 -12.168
> 2 0.121 5.188 -15.238
> 3 -12.168 -15.238 -2340.130
>
> INDIVIDUAL GROUPS INTERACTION
>
>
>
> GROUP INTRA INTER TOTAL
>
> 1 5.18 -12.05 -6.87
> 2 5.19 -15.12 -9.93
> 3 -2340.13 -27.41 -2367.53
>
>
> TOTAL -2329.76 -27.28 -2357.05
>
>
>
> .......................................................................
>
> So what is the exact significance of these groups here , how come they are
> 3
>
>
> waiting for your reply
>
>
> Gurpreet
>
>

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